Welcome to US-SOMO

Welcome to the US-SOMO website.

UltraScan Solution Modeler (US-SOMO) processes atomic and lower-resolution bead model representations of biological and other macromolecules to compute various hydrodynamic parameters, such as the sedimentation and diffusion coefficients, relaxation times and intrinsic viscosity, and small angle scattering curves, that contribute to our understanding of molecular structure in solution. Knowledge of biological macromolecules' structure aids researchers in understanding their function as a path to disease prevention and therapeutics for conditions such as cancer, thrombosis, Alzheimer's disease and others. US-SOMO provides a convergence of experimental, computational, and modeling techniques, in which detailed molecular structure and properties are determined from data obtained in a range of experimental techniques that, by themselves, give incomplete information.

Update 5 November 2018 US-SOMO revision 3167

An updated US-SOMO has been released. These include improvements to the layout for smaller screen sizes, a simplified installation for Windows, and a few bugfixes.
Click link in sidebar for "install" instructions.

Update 3 Oct 2018 US-SOMO revision 3165

An improved US-SOMO with updates to the HPLC-SAXS routines has been released. A tutorial will be held as part of the BioSAS: Advanced Applications course at SAS2018. Notes and special instructions for this tutorial are here. Click link in sidebar for "install" instructions.

Update 22 Jan 2018 US-SOMO revision 3141

An updated US-SOMO with an improved ZENO implemention, including support for multi-core processors on all operating systems has been released. This update includes improvements to the hydrodynamic section of US‑SOMO, adding a direct atom-to-beads utility (vdW), and to the small-angle scattering modules, such as the inclusion of an indirect Fourier transform method with a Bayesian approach for the computation of the distance distribution function P(r) vs. r in real space from scattering intensity as a function of momentum transfer I(q) vs. q in reciprocal space. Click link in sidebar for "install" instructions.

Intermediate Update 12 December 2017 US-SOMO revision 3112

US-SOMO has been integrated into UltraScan III versions 3.5 & 4.0. You can obtain these new versions here. This includes the newer faster and threaded version of 2ENO for all 64 bit platforms.

Update 17 July 2017 US-SOMO revision 3087

If you are attending the workshop at AUC 2017, please install the software beforehand.

Update 20 July 2016 US-SOMO revision 3087

A new version of US-SOMO with HPLC tools and sample data is available here. This includes updates as described in

There have also been multiple minor improvements to the interface for
the UltraScan III version, including a helpful directory history system
which remembers visited directories across sessions.

Note that the UltraScan II version of US-SOMO was previously
advanced from the UltraScan III version. These are now in sync
and will remain so until the eventual deprecation of the UltraScan II
version.

Please give it a try and let us know if you run into any problems.

Important Update 11 November 2013

(further updated 11 April 2014)

(updated to version 2504: 23 November 2013)

Dear UltraScan-SOMO users and newcomers:

The latest version of US-SOMO including the new HPLC SAXS tools is available here.
We will be preparing a geneal release before the ACA meeting where we have a dedicated session on HPLC-SAXS (4.2.4)
and a special tutorial session on the US-SOMO HPLC-SAXS tools (2.2.6).

US-SOMO is bundled as part of the UltraScan software. For all Linux, Windows, and Macintosh (running OSX 10.5 or older version), we recommend downloading the US-II version here.
For Macintosh users running OSX 10.6 or newer, we recommend downloading the US-III version here.

These files contains updated residues and will always be the latest versions.

They should be placed in the system ultrascan/etc directory.

Note: these may require administrator permissions to install on your system.

System

Typical location

OSX US3

/Applications/ultrascan3/etc

Linux US2

/usr/local/ultrascan/etc

Linux US3

/usr/local/ultrascan3/etc

Windows (EN) US2

\Program Files\ultrascan\etc

Windows (EN) US3

\Program Files\ultrascan3\etc

After correctly placing the file, the next startup of US-SOMO will request the installation of the files and will back up the current ones.
Again, this may require administrator privileges.

Important Update 3 March 2013

Dear UltraScan-SOMO users and newcomers:

Peter Zipper has recently discovered some errors in the distributed version of the somo.residue file of US-SOMO. I paste below his comments:

In my recent tests using Ultrascan 9.9 Rev. 1831 I encountered a discrepancy between the molecular weights of RNA chains as reported by Ultrascan and the results obtained from my programs. When I analyzed the discrepancy in more detail I could localize its origin very soon. I detected that in the Ultrascan file somo.residue the nucleobases are not represented with the correct number of hydrogen atoms but are lacking between 1 and 3 hydrogens.

In detail:

in adenine one hydrogen is missing at C2;

in cytosine one hydrogen is missing at C5 and one at C6;

in guanine one hydrogen is missing at N1 and two are missing at N2;

in uracil one hydrogen is missing at N3, C5, and C6, respectively;

in thymine one hydrogen is missing at N3 and one at C6.

I do not understand why these hydrogens are not taken into account in your somo.residue file. But perhaps you can give me a simple explanation.

As a matter of fact, Peter was absolutely correct, and I take full responsibility for that, it was sloppy entering on my part. I apologize for any inconvenience this might have caused, and I am grateful to Peter for having uncovered these mistakes. I have now corrected them, and new versions of the somo.residue and somo.atom files are made available for downloading (see the "After installation:" notes at the top of this webpage for instructions). Beside the corrections, the new somo.residue now contains hydroxyproline, more alternate names for nucleotides (wish there was a strict convention on PDB atoms naming to which all software adhered...), Triton X-100 (with different chain lengths), Mn and Mg ions, AMP, ATP, ATF, and explicit water of hydration (for SAXS simulations, the structures must hydrated using external programs). If you have coded for new atoms/residues using US-SOMO, you should pick those bits from your current tables and add them to the new tables, an operation that can be done using any text editor (however, should anyone feel uneasy to do so, you can send me your somo.atom and somo.residue files, and I will insert the extra residues/atoms in either the current distribution, or, if you want to keep it private, I will email the corrected files back to you).

Best wishes to you all, and happy hydrodynamic/SAS modeling with US-SOMO!

Mattia

Intermediate Release Announcement

Dear UltraScan-SOMO users and newcomers:

While a full new US-SOMO release is still in the making, we'd like to
announce an "intermediate" release of US-SOMO for Linux, Windows and
Mac systems. Besides several bug fixes, this version has many new
features, additions and improvements, among which are:

A revised somo.residue file in which the partial specific volumes of
inorganic ions have been re-calculated from the molar volumes values
present in Table III of Durchschlag and Zipper, Prog. Colloid
Polym. Sci. 94:20-39,1994. Previously, and erroneously, these psv
values were computed directly from the ions' radii. For some cations,
like Ca++ and Mg++, the psv assumes relatively large negative values
(which also required changes in the main program coding to handle
them). We apologize for this mistake. While the effect on proteins is
likely small, it is probably more relevant for peptides and nucleic
acids.

A revised Cluster access module. Access to some of the XSEDE
(formerly TeraGrid) resources and the Alamo cluster at the UTHSCSA is
now available. There are further improvements planned to this
facility, but it is basically functional to compute SAXS curves on
large numbers of structures and to perform discrete molecular dynamic
simulations. Cluster usage can now be granted to users upon
request. Hopefully, this will enable more users to take advantage of
these resources.

A functional PDB editor, which has some nice features like being
able to split up a multi model PDB file and join individual files.
You can also check your structure for errors with respect to the
US-SOMO residue table and search for alternate matching residues. It
is still under development, but is useable.

In the SAXS/SANS module, there are now multiple methods for
computing the scattering curve, including a full Debye (requiring
explicitly hydrated structures), and interface with CRYSOL (which
should be downloaded separately). There is also the ability to
compute the distance distribution function p(r) vs. r from structures
and a method to display a colored contribution of atoms to regions of
the p(r) in the molecular viewer. Best fit and least squares methods
of curves to experimental data are also included.

A model classifier, functional to rank batches of results from
hydrodynamic computations against experimental values is various ways.

We also offer another hydrodynamic computation method, Zeno, based
on the analogy between electrostatics and hydrodynamics (see the Zeno
website, http://www.stevens.edu/zeno/). We have not yet completed a
comparison of this method vs. our standard Garcia de la
Torre-Bloomfield method, but we plan to do this shortly. A newer
version will be available in the next release featuring faster
processing times.